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MIGEC: Molecular Identifier Guided Error Correction pipeline

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FEATURES

  • De-multiplexing, adapter trimming and read overlapping for NGS data. Extraction of UMI sequences
  • Assembly of consensuses for original molecules that entered library preparation by grouping reads with identical molecular identifiers
  • Mapping of V, D and J segments, extraction of CDR3 regions and clonotype assembly for all human and mouse immune receptors (TRA/TRB/TRG/TRD and IGH/IGL/IGK)
  • Additional filtering of hot-spot errors in CDR3 sequence
  • Flexible and straightforward batch processing
  • Currently all species-gene pairs that have germline sequences (based on IMGT) that allow CDR3 identification are supported
Species Gene
HomoSapiens TRA, TRB, TRG, TRD, IGL, IGK, IGH
MusMusculus TRB, TRG, TRD, IGL, IGK, IGH
MacacaMulatta TRB, IGK, IGH
OryctolagusCuniculus IGL, IGK, IGH
RattusNorvegicus IGL, IGH
CanisLupusFamiliaris TRB, TRG
SusScrofa IGL, IGK
BosTaurus TRD
MusSpretus IGL
GallusGallus TRB
AnasPlatyrhynchos TRB

Table of contents:

.. toctree::
   :maxdepth: 1

   install
   pipeline
   checkout
   histogram
   assemble
   cdrblast
   cdrfinal
   logs
   report
   post